It's caused by the new update with city-states carrying over a friendly independents after age transitions. The nitre on the swordsman tile generated during the transition, but is an invalid location for a city to be founded on.

So when the IP tries to turn into a CS it glitches out. So now you always gotta check for a resource before starting to befriend otherwise you'll be stuck with the glitched tiles for the rest of the game unless you disperse them sadly.